Shanghai is experiencing water supply problems caused by heavy pollution of its raw water supply, deficiencies in its treatment processes and water quality deteoriation in the distribution system. However, little attention has been paid these problems of water quality in raw water, water treatment and household drinking water. Based on water quality data we show that the raw water sources of the Huangpu River and the Changjiang (Yangtze River) estuary are polluted by microbes (TBC), eutrophication (TP, TN and NH3-N), heavy metals (Fe, Mn and Hg) and organic contamination (chemical oxygen demand [COD], detergent and volatile phenols [VP]). The average concentrations of these contaminants in the Huangpu River are almost double that of the Changjiang estuary forcing a rapid shift to the Changjiang estuary for raw water. In spite of filtering and treatment, TN, NH3-N, Fe, COD and chlorine maxima of the treated water and drinking water still exceed the Chinese National Standard (GB5749). We determine that the relevant threats from water source to household water in Shanghai are: 1) eutrophication arising from highly concentrated TN, TP, COD and algal density in the raw water; 2) increasing salinity in the river estuary, especially at the Qingcaosha Reservoir (currently the major freshwater source for Shanghai); 3) more than 50% of organic constituents and by-products remain in treated water; 4) bacteria and turbidity increase in the course of water delivery to users. The analysis presents an holistic assessment of the water quality threats to metropolitan Shanghai in relation to the city’s rapid development.